CUT and RUNTools: A flexible pipeline for CUT and RUN processing and footprint analysis

Abstract

We introduce CUT and RUNTools as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT and RUN primary cleavage data. CUT and RUNTools extracts endonuclease cut site information from sequences of short-read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT and RUN. CUT and RUNTools is available at https://bitbucket.org/qzhudfci/cutruntools/.